bio-polyploid-tools 0.1.0

Sign up to get free protection for your applications and to get access to all the features.
Files changed (92) hide show
  1. checksums.yaml +7 -0
  2. data/Gemfile +16 -0
  3. data/Gemfile.lock +67 -0
  4. data/README +21 -0
  5. data/Rakefile +61 -0
  6. data/VERSION +1 -0
  7. data/bin/bfr.rb +133 -0
  8. data/bin/count_variations.rb +36 -0
  9. data/bin/filter_blat_by_target_coverage.rb +15 -0
  10. data/bin/find_best_blat_hit.rb +32 -0
  11. data/bin/hexaploid_primers.rb +168 -0
  12. data/bin/homokaryot_primers.rb +155 -0
  13. data/bin/map_markers_to_contigs.rb +66 -0
  14. data/bin/markers_in_region.rb +42 -0
  15. data/bin/polymarker.rb +219 -0
  16. data/bin/snps_between_bams.rb +106 -0
  17. data/bio-polyploid-tools.gemspec +139 -0
  18. data/conf/defaults.rb +1 -0
  19. data/conf/primer3_config/dangle.dh +128 -0
  20. data/conf/primer3_config/dangle.ds +128 -0
  21. data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
  22. data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
  23. data/conf/primer3_config/interpretations/loops_i.dh +34 -0
  24. data/conf/primer3_config/interpretations/loops_i.ds +31 -0
  25. data/conf/primer3_config/interpretations/stack_i.dh +257 -0
  26. data/conf/primer3_config/interpretations/stack_i.ds +256 -0
  27. data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  28. data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  29. data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
  30. data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
  31. data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
  32. data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
  33. data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
  34. data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
  35. data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
  36. data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
  37. data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  38. data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  39. data/conf/primer3_config/loops.dh +30 -0
  40. data/conf/primer3_config/loops.ds +30 -0
  41. data/conf/primer3_config/stack.dh +256 -0
  42. data/conf/primer3_config/stack.ds +256 -0
  43. data/conf/primer3_config/stackmm.dh +256 -0
  44. data/conf/primer3_config/stackmm.ds +256 -0
  45. data/conf/primer3_config/tetraloop.dh +77 -0
  46. data/conf/primer3_config/tetraloop.ds +77 -0
  47. data/conf/primer3_config/triloop.dh +16 -0
  48. data/conf/primer3_config/triloop.ds +16 -0
  49. data/conf/primer3_config/tstack.dh +256 -0
  50. data/conf/primer3_config/tstack2.dh +256 -0
  51. data/conf/primer3_config/tstack2.ds +256 -0
  52. data/conf/primer3_config/tstack_tm_inf.ds +256 -0
  53. data/lib/bio/BFRTools.rb +698 -0
  54. data/lib/bio/BIOExtensions.rb +186 -0
  55. data/lib/bio/PolyploidTools/ChromosomeArm.rb +52 -0
  56. data/lib/bio/PolyploidTools/ExonContainer.rb +194 -0
  57. data/lib/bio/PolyploidTools/Marker.rb +175 -0
  58. data/lib/bio/PolyploidTools/PrimerRegion.rb +22 -0
  59. data/lib/bio/PolyploidTools/SNP.rb +681 -0
  60. data/lib/bio/PolyploidTools/SNPSequence.rb +56 -0
  61. data/lib/bio/SAMToolsExtensions.rb +284 -0
  62. data/lib/bio/db/exonerate.rb +272 -0
  63. data/lib/bio/db/fastadb.rb +164 -0
  64. data/lib/bio/db/primer3.rb +673 -0
  65. data/lib/bioruby-polyploid-tools.rb +25 -0
  66. data/test/data/BS00068396_51.fa +2 -0
  67. data/test/data/BS00068396_51_contigs.aln +1412 -0
  68. data/test/data/BS00068396_51_contigs.dnd +7 -0
  69. data/test/data/BS00068396_51_contigs.fa +8 -0
  70. data/test/data/BS00068396_51_exonerate.tab +6 -0
  71. data/test/data/BS00068396_51_genes.txt +14 -0
  72. data/test/data/LIB1716.bam +0 -0
  73. data/test/data/LIB1716.bam.bai +0 -0
  74. data/test/data/LIB1719.bam +0 -0
  75. data/test/data/LIB1719.bam.bai +0 -0
  76. data/test/data/LIB1721.bam +0 -0
  77. data/test/data/LIB1721.bam.bai +0 -0
  78. data/test/data/LIB1722.bam +0 -0
  79. data/test/data/LIB1722.bam.bai +0 -0
  80. data/test/data/S22380157.fa +16 -0
  81. data/test/data/S22380157.fa.fai +1 -0
  82. data/test/data/Test3Aspecific.csv +1 -0
  83. data/test/data/Test3Aspecific_contigs.fa +6 -0
  84. data/test/data/patological_cases5D.csv +1 -0
  85. data/test/data/short_primer_design_test.csv +10 -0
  86. data/test/data/test_primer3_error.csv +4 -0
  87. data/test/data/test_primer3_error_contigs.fa +10 -0
  88. data/test/test_bfr.rb +51 -0
  89. data/test/test_exon_container.rb +17 -0
  90. data/test/test_exonearate.rb +53 -0
  91. data/test/test_snp_parsing.rb +40 -0
  92. metadata +201 -0
data/conf/primer3_config/stackmm.dh ADDED
@@ -0,0 +1,256 @@
1
+ inf
2
+ inf
3
+ inf
4
+ 4700
5
+ inf
6
+ inf
7
+ inf
8
+ 7600
9
+ inf
10
+ inf
11
+ inf
12
+ 3000
13
+ 1200
14
+ 2300
15
+ -600
16
+ inf
17
+ inf
18
+ inf
19
+ -2900
20
+ inf
21
+ inf
22
+ inf
23
+ -700
24
+ inf
25
+ inf
26
+ inf
27
+ 500
28
+ inf
29
+ 5300
30
+ -10
31
+ inf
32
+ 700
33
+ inf
34
+ -900
35
+ inf
36
+ inf
37
+ inf
38
+ 600
39
+ inf
40
+ inf
41
+ inf
42
+ -4000
43
+ inf
44
+ inf
45
+ -700
46
+ inf
47
+ -3100
48
+ 1000
49
+ 1200
50
+ inf
51
+ inf
52
+ inf
53
+ 5300
54
+ inf
55
+ inf
56
+ inf
57
+ -700
58
+ inf
59
+ inf
60
+ inf
61
+ inf
62
+ -1200
63
+ -2500
64
+ -2700
65
+ inf
66
+ inf
67
+ inf
68
+ 3400
69
+ inf
70
+ inf
71
+ inf
72
+ 6100
73
+ -900
74
+ 1900
75
+ -700
76
+ inf
77
+ inf
78
+ inf
79
+ inf
80
+ 1000
81
+ inf
82
+ inf
83
+ 5200
84
+ inf
85
+ inf
86
+ inf
87
+ 3600
88
+ inf
89
+ 600
90
+ -1500
91
+ inf
92
+ -800
93
+ inf
94
+ inf
95
+ 5200
96
+ inf
97
+ inf
98
+ 1900
99
+ inf
100
+ inf
101
+ inf
102
+ -1500
103
+ inf
104
+ inf
105
+ -4000
106
+ inf
107
+ -4900
108
+ -4100
109
+ inf
110
+ -1500
111
+ inf
112
+ inf
113
+ 2300
114
+ inf
115
+ inf
116
+ inf
117
+ -10
118
+ inf
119
+ inf
120
+ inf
121
+ inf
122
+ -1500
123
+ -2800
124
+ -5000
125
+ -1200
126
+ inf
127
+ inf
128
+ inf
129
+ inf
130
+ inf
131
+ inf
132
+ 700
133
+ -2900
134
+ 5200
135
+ -600
136
+ inf
137
+ inf
138
+ inf
139
+ inf
140
+ 1600
141
+ inf
142
+ inf
143
+ inf
144
+ -1300
145
+ inf
146
+ inf
147
+ -600
148
+ inf
149
+ -700
150
+ 3600
151
+ inf
152
+ 2300
153
+ inf
154
+ inf
155
+ -6000
156
+ inf
157
+ inf
158
+ inf
159
+ -4400
160
+ inf
161
+ inf
162
+ -700
163
+ inf
164
+ inf
165
+ 500
166
+ inf
167
+ -6000
168
+ 3300
169
+ inf
170
+ -4900
171
+ inf
172
+ inf
173
+ inf
174
+ -2800
175
+ inf
176
+ 5800
177
+ -600
178
+ inf
179
+ inf
180
+ inf
181
+ inf
182
+ 5200
183
+ -4400
184
+ -2200
185
+ -3100
186
+ inf
187
+ inf
188
+ inf
189
+ -2500
190
+ inf
191
+ 4100
192
+ inf
193
+ 4700
194
+ 3400
195
+ 700
196
+ inf
197
+ inf
198
+ inf
199
+ inf
200
+ 1200
201
+ inf
202
+ inf
203
+ inf
204
+ -100
205
+ inf
206
+ inf
207
+ inf
208
+ 200
209
+ 7600
210
+ 6100
211
+ inf
212
+ 1200
213
+ inf
214
+ inf
215
+ 2300
216
+ inf
217
+ inf
218
+ inf
219
+ 3300
220
+ inf
221
+ inf
222
+ inf
223
+ -2200
224
+ inf
225
+ 3000
226
+ inf
227
+ 1600
228
+ -100
229
+ inf
230
+ -800
231
+ inf
232
+ inf
233
+ inf
234
+ -4100
235
+ inf
236
+ -1400
237
+ inf
238
+ -5000
239
+ inf
240
+ inf
241
+ inf
242
+ 1000
243
+ -1300
244
+ 200
245
+ 700
246
+ inf
247
+ inf
248
+ inf
249
+ 1000
250
+ inf
251
+ 5800
252
+ inf
253
+ -2700
254
+ inf
255
+ inf
256
+ inf
data/conf/primer3_config/stackmm.ds ADDED
@@ -0,0 +1,256 @@
1
+ inf
2
+ inf
3
+ inf
4
+ 12.9
5
+ inf
6
+ inf
7
+ inf
8
+ 20.2
9
+ inf
10
+ inf
11
+ inf
12
+ 7.4
13
+ 1.7
14
+ 4.6
15
+ -2.3
16
+ inf
17
+ inf
18
+ inf
19
+ -9.8
20
+ inf
21
+ inf
22
+ inf
23
+ -3.8
24
+ inf
25
+ inf
26
+ inf
27
+ 3.2
28
+ inf
29
+ 14.6
30
+ -4.4
31
+ inf
32
+ 0.2
33
+ inf
34
+ -4.2
35
+ inf
36
+ inf
37
+ inf
38
+ 0.6
39
+ inf
40
+ inf
41
+ inf
42
+ -13.2
43
+ inf
44
+ inf
45
+ -2.3
46
+ inf
47
+ -9.5
48
+ 0.9
49
+ 1.7
50
+ inf
51
+ inf
52
+ inf
53
+ 14.6
54
+ inf
55
+ inf
56
+ inf
57
+ -2.3
58
+ inf
59
+ inf
60
+ inf
61
+ inf
62
+ -6.2
63
+ -8.3
64
+ -10.8
65
+ inf
66
+ inf
67
+ inf
68
+ 8.0
69
+ inf
70
+ inf
71
+ inf
72
+ 16.4
73
+ -4.2
74
+ 3.7
75
+ -2.3
76
+ inf
77
+ inf
78
+ inf
79
+ inf
80
+ 0.7
81
+ inf
82
+ inf
83
+ 14.2
84
+ inf
85
+ inf
86
+ inf
87
+ 8.9
88
+ inf
89
+ -0.6
90
+ -7.2
91
+ inf
92
+ -4.5
93
+ inf
94
+ inf
95
+ 13.5
96
+ inf
97
+ inf
98
+ 3.7
99
+ inf
100
+ inf
101
+ inf
102
+ -7.2
103
+ inf
104
+ inf
105
+ -13.2
106
+ inf
107
+ -15.3
108
+ -11.7
109
+ inf
110
+ -6.1
111
+ inf
112
+ inf
113
+ 4.6
114
+ inf
115
+ inf
116
+ inf
117
+ -4.4
118
+ inf
119
+ inf
120
+ inf
121
+ inf
122
+ -6.1
123
+ -8.0
124
+ -15.8
125
+ -6.2
126
+ inf
127
+ inf
128
+ inf
129
+ inf
130
+ inf
131
+ inf
132
+ 0.7
133
+ -9.8
134
+ 14.2
135
+ -1.0
136
+ inf
137
+ inf
138
+ inf
139
+ inf
140
+ 3.6
141
+ inf
142
+ inf
143
+ inf
144
+ -5.3
145
+ inf
146
+ inf
147
+ -1.0
148
+ inf
149
+ -3.8
150
+ 8.9
151
+ inf
152
+ 5.4
153
+ inf
154
+ inf
155
+ -15.8
156
+ inf
157
+ inf
158
+ inf
159
+ -12.3
160
+ inf
161
+ inf
162
+ -2.3
163
+ inf
164
+ inf
165
+ 3.2
166
+ inf
167
+ -15.8
168
+ 10.4
169
+ inf
170
+ -15.3
171
+ inf
172
+ inf
173
+ inf
174
+ 80
175
+ inf
176
+ 16.3
177
+ 23
178
+ inf
179
+ inf
180
+ inf
181
+ inf
182
+ 13.5
183
+ -12.3
184
+ -8.4
185
+ -9.5
186
+ inf
187
+ inf
188
+ inf
189
+ -8.3
190
+ inf
191
+ 9.5
192
+ inf
193
+ 12.9
194
+ 8.0
195
+ 0.7
196
+ inf
197
+ inf
198
+ inf
199
+ inf
200
+ 0.7
201
+ inf
202
+ inf
203
+ inf
204
+ -1.7
205
+ inf
206
+ inf
207
+ inf
208
+ -1.5
209
+ 20.2
210
+ 16.4
211
+ inf
212
+ 0.7
213
+ inf
214
+ inf
215
+ 5.4
216
+ inf
217
+ inf
218
+ inf
219
+ 10.4
220
+ inf
221
+ inf
222
+ inf
223
+ -8.4
224
+ inf
225
+ 7.4
226
+ inf
227
+ 3.6
228
+ -1.7
229
+ inf
230
+ -4.5
231
+ inf
232
+ inf
233
+ inf
234
+ -11.7
235
+ inf
236
+ -6.2
237
+ inf
238
+ -15.8
239
+ inf
240
+ inf
241
+ inf
242
+ -7
243
+ -5.3
244
+ -1.5
245
+ 0.2
246
+ inf
247
+ inf
248
+ inf
249
+ 0.9
250
+ inf
251
+ 16.3
252
+ inf
253
+ -10.8
254
+ inf
255
+ inf
256
+ inf